Dear @panchyni @shinhanshiu
Hello! I am very interested in pseudogenes; and have read the introductory part of your paper on pseudogenes published in 2009. Now I have a question mainly having to do with the association of LTR retrotransposons (including transposons) with pseudogenes. As we know, transposons may be inserted in various parts of the genome. For example, this is shown in Figure 6C and Figure S7 in our recent paper on LTR transposons in Rhododendron ((https://onlinelibrary.wiley.com/doi/10.1111/plb.13532)) (parts are shown in the figure below). Frequently, LTRs overlap genes, but the overlap varies. For example, the overlap is in the CDS region, the introns, or the UTR region. Now I would like to ask, according to the "concept of pseudogene formation" described in your paper, which of the above situations would/could easily lead to the formation of pseudogenes (since there seems to be no discussion of transposable elements in the original paper)? To my knowledge, it is possible that when LTRs are inserted in the intronic portion of a coding gene, there may not be pseudogenes.
This figure roughly reflects the insertion of some LTRs into genes. The arrows in the figure show the transcription start points of LTRs. It can be seen that some LTRs are inserted in either exon parts or intron parts. Some of the lower case letters in the diagram reflect the type of insertion of the LTRs, e.g. i: insertion in an intronic part. More details can be found at: https://onlinelibrary.wiley.com/doi/10.1111/plb.13532.
How do you think about this issue?
BEST!!!
wen
Dear @panchyni @shinhanshiu
Hello! I am very interested in pseudogenes; and have read the introductory part of your paper on pseudogenes published in 2009. Now I have a question mainly having to do with the association of LTR retrotransposons (including transposons) with pseudogenes. As we know, transposons may be inserted in various parts of the genome. For example, this is shown in Figure 6C and Figure S7 in our recent paper on LTR transposons in Rhododendron ((https://onlinelibrary.wiley.com/doi/10.1111/plb.13532)) (parts are shown in the figure below). Frequently, LTRs overlap genes, but the overlap varies. For example, the overlap is in the CDS region, the introns, or the UTR region. Now I would like to ask, according to the "concept of pseudogene formation" described in your paper, which of the above situations would/could easily lead to the formation of pseudogenes (since there seems to be no discussion of transposable elements in the original paper)? To my knowledge, it is possible that when LTRs are inserted in the intronic portion of a coding gene, there may not be pseudogenes.
This figure roughly reflects the insertion of some LTRs into genes. The arrows in the figure show the transcription start points of LTRs. It can be seen that some LTRs are inserted in either exon parts or intron parts. Some of the lower case letters in the diagram reflect the type of insertion of the LTRs, e.g. i: insertion in an intronic part. More details can be found at:https://onlinelibrary.wiley.com/doi/10.1111/plb.13532.How do you think about this issue?
BEST!!!
wen